Massive Gene Database Planned in California

Massive Gene Database Planned in California

Spit kit: Genetic data from a diverse group of 100,000 California patients will be gleaned from samples of saliva, captured in kits like this one.

Plans for genetic analyses of 100,000 older Californians–the first time genetic data will be generated for such a large and diverse group–will accelerate research into environmental and genetic causes of disease, researchers say.

“This is a force multiplier with respect to genome-wide association studies,” says Cathy Schaefer, a research scientist at Kaiser Permanente, a health-care provider based in Oakland, CA, whose patients will be involved. Researchers will be able to study the data and seek insights into the interplay between genes, the environment, and disease, thanks to access to detailed electronic health records, patient surveys, and even records of environmental conditions where the patients live and work.

“The importance of this project is that it will, almost overnight–well, in two years–produce a very large amount of genetic and phenotypic data that a large number of investigators and scientists can begin asking questions of, rather than having to gather data first,” Schaefer says.

The effort will make use of existing saliva samples taken from California patients, whose average age is 65. Their DNA will be analyzed for 700,000 genetic variations called single-nucleotide polymorphisms, or SNPs, using array analysis technology from Affymetrix in Santa Clara, CA. Through the National Institutes of Health (NIH), the resulting information will be available to other researchers, along with a trove of patient data including patients’ Kaiser Permanente electronic health records, information about the air and water quality in their neighborhoods, and surveys about their lifestyles.

The result will be the largest genetic health research platform of its kind, says Schaefer, who directs Kaiser Permanente’s research program on genes, the environment, and health. The study is being undertaken together with the University of California, San Francisco (UCSF), with a $25 million, two-year NIH grant that tapped federal stimulus funds allocated earlier this year.

The potential for study is nearly limitless. Researchers will likely seek the genetic influences that determine why some people suffering from, say, cardiovascular disease and type 2 diabetes deteriorate more rapidly than others; and tease out which genetic factors reduce the effectiveness of various drugs or, indeed, make them hazardous, Schaefer says. As doctors obtain more such insights, this will allow them to tailor drug regimens and focus resources on higher-risk patients.

Given the high average age of the group, the platform will also be a boon to studying diseases of aging. “One might want to ask,” Schaefer says, “what are the genetic influences on changes in blood pressure as people age, and how are those changes in blood pressure related to diseases of aging, like stroke and Alzheimer’s and other cardiovascular diseases?”